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Web-enabled and Cross-platform SAM via Shiny

This version of SAM provided adds a web interface using Shiny.

Install the current version of the package, after removing any older versions you may have already installed. Later, when this package makes it to CRAN, you will install it the usual way.

The web interface is invoked via:

library(samr)
runSAM()

That will bring up a browser window with a user interface. More details are provided in the manual sam.pdf in this directory

Note that users should use Firefox or Chrome as the _default_browser on Windows: IE will not work.

Michael Seo

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Version

Install

install.packages('samr')

Monthly Downloads

546

Version

3.0

License

LGPL

Maintainer

Last Published

October 16th, 2018

Functions in samr (3.0)

runSAM

Run the sam webapp
SAM

Significance analysis of microarrays - simple user interface
SAMseq

Significance analysis of sequencing data - simple user interface
samr.plot

Make Q-Q plot for SAM analysis
samr.pvalues.from.perms

Report estimated p-values for each gene, from a SAM analysis
samr.estimate.depth

estimate the sequencing depth
samr-internal

Internal samr functions
samr.missrate

Estimate the miss rate table for a SAM analysis
samr.norm.data

output normalized sequencing data
samr.compute.delta.table

Compute delta table for SAM analysis
samr.compute.siggenes.table

Compute significant genes table
samr.tail.strength

Estimate tail strength for a dataset, from a SAM analysis
samr.assess.samplesize

Assess the sample size for a SAM analysis
samr.assess.samplesize.plot

Make a plot of the results from samr.assess.samplesize
samr

Significance analysis of microarrays